Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2418 to 2467 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2418	antithrombin-iii precursor (atiii) (pro0309). [source:swissprot;acc:p01008]	218.2	218.984	1.00359	
2419	translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q14232]	218.2	218.984	1.00359	
2420	squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [source:swissprot;acc:p29508]	218.2	218.984	1.00359	
2421	apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [source:refseq;acc:nm_032797]	210.205	209.454	1.00359	
2422	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [source:swissprot;acc:q13133]	218.2	218.984	1.00359	
2423	histone deacetylase 5 (hd5) (antigen ny-co-9). [source:swissprot;acc:q9uql6]	220.682	221.471	1.00358	
2424	histone deacetylase 4 (hd4). [source:swissprot;acc:p56524]	220.682	221.472	1.00358	
2425	histone deacetylase 9 (hd9) (hd7b) (hd7). [source:swissprot;acc:q9ukv0]	220.682	221.472	1.00358	
2426	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	212.374	211.618	1.00357	
2427	proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [source:swissprot;acc:p25788]	212.374	211.618	1.00357	
2428	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [source:swissprot;acc:p11766]	192.871	193.555	1.00355	
2429	esterase d (ec 3.1.1.1). [source:swissprot;acc:p10768]	192.871	193.555	1.00355	
2430	epsin 1; eh domain-binding mitotic phosphoprotein. [source:refseq;acc:nm_013333]	217.873	218.644	1.00354	
2431	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [source:swissprot;acc:p25787]	213.048	212.3	1.00352	
2432	26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [source:swissprot;acc:q15008]	215.807	216.556	1.00347	
2433	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	217.366	218.117	1.00346	
2434	methylenetetrahydrofolate reductase (ec 1.5.1.20). [source:swissprot;acc:p42898]	213.021	212.286	1.00346	
2435	zinc-finger protein zpr1 (zinc finger protein 259). [source:swissprot;acc:o75312]	217.366	218.117	1.00346	
2436	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [source:swissprot;acc:q05639]	217.366	218.117	1.00346	
2437	guanylate kinase (ec 2.7.4.8) (gmp kinase). [source:swissprot;acc:q16774]	219.361	220.116	1.00344	
2438	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [source:swissprot;acc:p25789]	214.049	213.323	1.0034	
2439	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [source:swissprot;acc:p31946]	220.681	221.425	1.00337	
2440	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [source:swissprot;acc:o43242]	217.645	218.376	1.00336	
2441	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [source:swissprot;acc:p13804]	180.137	180.732	1.0033	
2442	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [source:swissprot;acc:p49848]	204.419	203.748	1.00329	
2443	ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [source:swissprot;acc:p50550]	217.073	216.364	1.00328	
2444	zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [source:swissprot;acc:q9hc78]	206.086	206.753	1.00324	
2445	kruppel-related zinc finger protein hckrox. [source:refseq;acc:nm_015872]	206.088	206.756	1.00324	
2446	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	182.272	181.683	1.00324	
2447	peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [source:swissprot;acc:o00628]	206.084	206.752	1.00324	
2448	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [source:swissprot;acc:p23378]	212.446	211.766	1.00321	
2449	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [source:swissprot;acc:o95674]	204.717	205.371	1.00319	
2450	proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [source:swissprot;acc:p28072]	213.85	213.177	1.00316	
2451	secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	204.688	205.333	1.00315	
2452	secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	204.688	205.333	1.00315	
2453	secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	204.688	205.332	1.00315	
2454	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [source:swissprot;acc:q9ukg4]	204.683	205.326	1.00314	
2455	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [source:swissprot;acc:q8wwt9]	204.683	205.326	1.00314	
2456	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	204.683	205.326	1.00314	
2457	vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [source:swissprot;acc:p46459]	213.588	212.92	1.00314	
2458	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	204.683	205.326	1.00314	
2459	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	204.653	205.286	1.00309	
2460	pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	235.812	235.088	1.00308	
2461	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [source:refseq;acc:nm_006749]	235.812	235.088	1.00308	
2462	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [source:swissprot;acc:p14324]	235.812	235.088	1.00308	
2463	protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	235.812	235.088	1.00308	
2464	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [source:refseq;acc:nm_005415]	235.812	235.088	1.00308	
2465	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	235.812	235.088	1.00308	
2466	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	235.812	235.088	1.00308	
2467	suppressor of fused. [source:refseq;acc:nm_016169]	235.812	235.088	1.00308	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/